rs1516320

Variant names:

• chr3-34643-C-T
• rs1516320

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.789 in 152,112 control chromosomes in the GnomAD database, including 47,599 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (47599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119889 AN: 151994 Hom.: 47546 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.798

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.789 AC: 120001 AN: 152112 Hom.: 47599 Cov.: 32 AF XY: 0.790 AC XY: 58763 AN XY: 74358

African (AFR) AF: 0.844 AC: 34997 AN: 41478

American (AMR) AF: 0.847 AC: 12944 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2409 AN: 3472

East Asian (EAS) AF: 0.943 AC: 4885 AN: 5178

South Asian (SAS) AF: 0.701 AC: 3374 AN: 4810

European-Finnish (FIN) AF: 0.807 AC: 8531 AN: 10574

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50378 AN: 68002

Other (OTH) AF: 0.795 AC: 1679 AN: 2112

Alfa AF: 0.764 Hom.: 20194

Bravo AF: 0.796

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.76
PhyloP100		-0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1516320; hg19: chr3-76317;